Peter A. Bandettini - fMRI (The MIT Press Essential Knowledge series

The MIT Press Essential Knowledge Series

A complete list of the titles in this series appears at the back of this book.

Peter Bandettini

The MIT Press | Cambridge, Massachusetts | London, England

2020 Massachusetts Institute of Technology

All rights reserved. No part of this book may be reproduced in any form by any electronic or mechanical means (including photocopying, recording, or information storage and retrieval) without permission in writing from the publisher.

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Library of Congress Cataloging-in-Publication Data

Names: Bandettini, P. A. (Peter A.), author.

Title: fMRI / Peter A. Bandettini.

Description: Cambridge, MA : MIT Press, [2020] | Series: The MIT Press essential knowledge series | Includes bibliographical references and index.

Identifiers: LCCN 2019013953 | ISBN 9780262538039 (paperback : alk. paper)

Subjects: LCSH: BrainMagnetic resonance imaging. | Magnetic resonance imaging.

Classification: LCC RC386.6.M34 B36 2020 | DDC 616.8/047548dc23

LC record available at https://lccn.loc.gov/2019013953

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The MIT Press Essential Knowledge series offers accessible, concise, beautifully produced pocket-size books on topics of current interest. Written by leading thinkers, the books in this series deliver expert overviews of subjects that range from the cultural and the historical to the scientific and the technical.

In todays era of instant information gratification, we have ready access to opinions, rationalizations, and superficial descriptions. Much harder to come by is the foundational knowledge that informs a principled understanding of the world. Essential Knowledge books fill that need. Synthesizing specialized subject matter for nonspecialists and engaging critical topics through fundamentals, each of these compact volumes offers readers a point of access to complex ideas.

Bruce Tidor

Professor of Biological Engineering and Computer Science

Massachusetts Institute of Technology

In taking the first step and picking up this book, you may be wondering if this is just another book on fMRI (functional magnetic resonance imaging). To answer: This is not just another book on fMRI. While it contains all the basics and some of the more interesting advanced methods and concepts, it is imbued, for better or worse, with my unique perspective on the field. I was fortunate to be in the right place at the right time when fMRI first began. I was a graduate student at the Medical College of Wisconsin looking for a project. Thanks in large part to Eric Wong, my brilliant fellow graduate student who had just developed, for his own non-fMRI purposes, the hardware and pulse sequences essential to fMRI, and my co-advisors Scott Hinks and Jim Hyde who gave me quite a bit of latitude to find my own project, we were ready to perform fMRI before the first results were publicly presented by the Massachusetts General Hospital group on August 12, 1991, at the Society for Magnetic Resonance Meeting in San Francisco. After that meeting, I started doing fMRI, and in less than a month I saw my motor cortex light up when I tapped my fingers. As a graduate student, it was a mind-blowingly exciting timeto say the least. My PhD thesis was on fMRI contrast mechanisms, models, paradigms, and processing methods. Ive been developing and using fMRI ever since. Since 1999, I have been at the National Institute of Mental Health, as chief of the Section on Functional Imaging Methods and director of the Functional MRI Core Facility that services over thirty principle investigators. This facility has grown to five scannersone 7T and four 3Ts.

Thousands of researchers in the United States and elsewhere are fortunate that the National Institutes of Health (NIH) has provided generous support for fMRI development and applications continuously over the past quarter century. The technique has given us an unprecedented window into human brain activation and connectivity in healthy and clinical populations. However, fMRI still has quite a long way to go toward making impactful clinical inroads and yielding deep insights into the functional organization and computational mechanisms of the brain. It also has a long way to go from group comparisons to robust individual classifications.

The field is fortunate because in 1996, fMRI capability (high-speed gradients and time-series echo planar imaging) became available on standard clinical scanners. The thriving clinical MRI market supported and launched fMRI into its explosive adoption worldwide. Now an fMRI-capable scanner was in just about every hospital and likely had quite a bit of cheap free time for a research team to jump on late at night or on a weekend to put a subject in the scanner and have them view a flashing checkerboard or tap their fingers.

Many cognitive neuroscientists changed their career paths entirely in order to embrace this new noninvasive, relatively fast, sensitive, and whole-brain method for mapping human brain function. Clinicians took notice, as did neuroscientists working primarily with animal models using more invasive techniques. It looked like fMRI had potential. The blood oxygen leveldependent (BOLD) signal change was simply magic. It just workedevery time. That 5% signal change started revealing, at an explosive rate, what our brains were doing during an ever-growing variety and number of tasks and stimuli, and then during rest.

Since the exciting beginnings of fMRI, the field has grown in different ways. The acquisition and processing methods have become more sophisticated, standardized, and robust. The applications have moved from group comparisons where blobs were comparedsimple cartographyto the machine learning analysis of massive data sets that are able to draw out subtle individual differences in connectivity between individuals. In the end, its still cartography because we are far from looking at neuronal activity directly, but we are getting much better at gleaning ever more subtle and useful information from the details of the spatial and temporal patterns of the signal change. While things are getting more standardized and stable on one level, elsewhere there is a growing amount of innovation and creativity, especially in the realm of post-processing. The field is just starting to tap into the fields of machine learning, network science, and big data processing.

The perspective I bring to this book is similar to that of many who have been on the front lines of fMRI methodology researchtesting new processing approaches and new pulse sequences, tweaking something here or there, trying to quantify the information and minimize the noise and variability, attempting to squeeze every last bit of interesting information from the time seriesand still working to get rid of those large vessel effects!

This book reflects my perspective of fMRI as a physicist and neuroscientist who is constantly thinking about how to make fMRI bettereasier, more informative, and more powerful. I attempt to cover all the essential details fully but without getting bogged down in jargon and complex concepts. I talk about trade-offsthose between resolution and time and sensitivity, between field strength and image quality, between specificity and ease of use.

I also dwell a bit on the major milestonesthe start of resting state fMRI, the use and development of event-related fMRI, the ability to image columns and layers, the emergence of functional connectivity imaging and machine learning approachesas reflecting on these is informative and entertaining. As a firsthand participant and witness to the emergence of these milestones, I aim to provide a nuanced historical context to match the science.